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fbtwitterlinkedinvimeoflicker grey 14rssslideshare1
Davies, Owen R.
Languages: English
Types: Doctoral thesis
Subjects: QC
In this thesis an efficient method has been developed for calculating the electronic structure and conductance of large biological molecules. The embedding method has been adapted to allow the splitting of large molecules such as DNA into smaller component blocks, completely preserving the information of the macro-system. The computational time required for this method increases as O(N) with the size of the system, instead of the traditional O(N3). The semi-empirical extended Huckel theory is used to describe the electron wavefunctions within a tight-binding scheme, taking the effect of the metal-molecule contacts into account. Presented in this thesis are the results for several different DNA molecules and structures. It has been determined that the transmission through DNA depends sensitively on the energy at which it is evaluated, and the atoms to which the metallic leads are connected. It is also found that poly(G)-poly(C) DNA conducts charge better than DNA with mixed bases, and that energy-minimised DNA with less structural disorder conducts better than DNA obtained from x-ray diffraction experiments. The electrical conduction of DNA that has undergone stretching has been investigated, and the distorted structure gives very small currents. The embedding method has also been applied to the small aromatic molecule OPE, to determine its electronic properties. Metallic conductivity is found for this molecule, and it is able to carry currents 1000 times greater than DNA, giving possible applications in molecular electronics.
  • The results below are discovered through our pilot algorithms. Let us know how we are doing!

    • [1] D. Normile. Science, 293(5531):787, 2001.
    • [2] L. B. Sivitz. Science News, 158(22) :350, 2000.
    • [3] H. Shirakawa, E. J. Louis, A. G. Macdiarmid, C. K.Chiang, and A. J. Heeger. J. C. S. Chem. Comm., pages 578-580, 1977.
    • [4] J. E. McGinness, P. M. Corry, and P. Proctor.Science,183:853-855, 1974.
    • [5] S. Iijima. Nature, 354(56), 1991.
    • [6] M. Yu, O. Lourie, M. J. Dyer, K. Moloni, T. F. Kelly, and R. S. Ruoff. Science, 287:637-640, 2000.
    • [7] T. Yildirim, O. Giilseren, Q. Kilig, and S. Ciraci. Phys. Rev. B, 62(19), 2000.
    • [8] A. Bachtold, M. S. Fuhrer, S. Plyasunov, M. Forero, E. M. Anderson, A. Zettl, and P. L. McEwen. Phys. Rev. Lett., 84(26):6082-6085, 2000.
    • [9] J. W. G. Wildoer et al. Nature, 391:59, 1998.
    • [10] C. W. Tang and S. A. Slyke. Appl. Phys. Lett., 51(913), 1987.
    • [11] L. M. Adleman. Science, 266(5187): 1021-1024, 1994.
    • [12] Y. Benenson, T. Paz-Elizur, R. Adax, E. Keinan, Z. Livneh, and E. Shapiro. Nature, 414(6862):430-434, 2001.
    • [13] J. Fritz et al. Science, 288(5464):316-318, 2000.
    • [14] J. Chen and N. C. Seeman. Nature, 350(6319):631-633, 1991.
    • [15] N. C. Seeman. Nature, 421(6921):427-431, 2003.
    • [16] D. D. Eley and D. I. Spivey. Trans. Faraday Soc., 58:411-415, 1962.
    • [17] D. Van Lith, J. M. Warman, M. P. de Haas, A. Hummel, and C. Prinsen. J. Chem. Soc., Faraday Trans., pages 2933-2943, 1986.
    • [18] M. E. Nunez, D. B. Hall, and J. K. Barton. Chemistry and Biology, 6(85), 1999.
    • [19] C. J. Murphy, M. R. Arkin, Y. Jenkins, N. D. Ghatlia, S. H. Bossman, N. J. Turro, and J. K. Barton. Science, 262(1025), 1993.
    • [20] E. Braun, Y. Elchen, U. Sivan, and G. Ben-Yoseph. Nature, 391:775, 1998.
    • [21] H. W. Fink and C. Schonenberger. Nature, 398(6726):407-410, 1999.
    • [22] D. Porath, A. Bezryadin, S. de Vries, and C. Dekker. Nature, 403:635-638, 2000.
    • [23] A. Y. Kasumov et al. Science, 291 (5502):280-282, 2001.
    • [24] L. Helman. Science, 293:583-585, 2001.
    • [25] A. R. Butler et al. Nature Biotechnology, 20(7):713-716, 2002.
    • [26] F. Kreppel, V. Biermann, and S. Kochanek. 13(10):1151-1156, 2002.
    • [29] J. Watson and F. Crick. Nature, 171 (4356):373-374, 1953.
    • [30] K. W. Hipps. Science,, 294:536-537, 2001.
    • [31] G. Cuniberti, L. Craco, D. Porath, and C. Dekker. Phys. Rev. B, 65:241314, 2002.
    • [32] F. Moreno-Herrero, P. Herrero, F. Moreno, J. Colchero, C. Gomez-Navaro, J. Gomez-Herrero, and A. M. Baro. Nanotechnology, 14(2): 128-133, 2003.
    • [33] P. Lincoln, E. Tuite, and B. Norden. J. Am. Chem. Soc., 119(1454), 1997.
    • [34] S. Priyadarshy, S. M. Risser, and D. N. Beratan. J. Biol. Inorg. Chem., 3(196), 1998.
    • [35] N. J.Turro and J. K. Barton. J. Biol. Inorg. Chem., 3(201), 1998.
    • [39] T. T. Williams, D. T. Odom, and J. K. Barton. J. Am. Chem. Soc., 122:9048- 9049, 2000.
    • [40] C. Gomez-Navarro, M. Alvarez A. Gil, P. J. de Pablo, F. Moreno-Herrero, I. Horcas, R. Fernandez-Sanchez, J. Colchero, J. Gomez Herrero, and A. M. Baro. Nanotechnology, 13(314), 2002.
    • [41] A. Gil, P. J. de Pablo, J. Colchero, J. Gomez Herrero, and A. M. Baro. Nanotechnology, 13(309), 2002.
    • [42] C. Gomez-Navarro, F. Moreno-Herrero, P. J. de Pablo, J. Colchero, J. Gomez Herrero, and A. M. Baro. Proc. Nat. Acad. Sci., 99(8484), 2002.
    • [43] M. Bockrath, N. Markovic, A. Shepard, M. Tinkham, L. Gurevich, L. P. Kouwenhoven, M. W. Wu, and L. L. Sohn. Nano. Lett., 2(187), 2002.
    • [44] P. Tran, B. Alavi, and G. Gruner. Phys. Rev. Lett., 85(7): 1564-1567, 1999.
    • [45] P. J. de Pablo, F. Moreno-Herrero, J. Colchero, J. Gomez Herrero, P. Herrero, A. M. Baro, P. Ordejon, J. M Soler, and E. Artacho. Phys. Rev. Lett., 85(23):4992-4995, 2000.
    • [46] A. J. Storm, J. van Noort, S. de Vries, and C. Dekker. Appl. Phys. Lett., 79(23):3881-3883, 2001.
    • [47] Y. Zhang, R. H. Austin, J. Kraeft, E. C. Cox, and N. P. Ong. Phys. Rev. Lett., 89(198102), 2002.
    • [48] H. Tabata L. Cai and T. Kawai. Appl. Phys. Lett., 77(19), 2000.
    • [49] H. Watanabe, C. Manabe, T. Shigematsu, K. Shimotani, and M. Shimizu. Appl. Phys. Lett., 79(15) :2462-2464, 2001.
    • [50] K. H. Yoo, D. H. Ha, J. O. Lee, J. W. Park, Jinhee Kim, J. J. Kim, H. Y. Lee, T. Kawai, and Han Yong Choi. Phys. Rev. Lett., 87(19), 2001.
    • [51] J. S. Hwang, K. J. Kang, D. Ahn, G. S. Lee, D. J. Ahn, and S. W. Hwang. Appl. Phys. Lett., 81(6): 1134-1136, 2002.
    • [52] J. M. Ziman. Principles of the theory of solids. Camb. Univ. Press, 1965.
    • [53] E. M. Conwell and S. V. Rakhmanova. Proc. Natl. Acad. Sci., 97(9):4556- 4560, 2000.
    • [54] F. Mandl. Quantum mechanics. Wiley, page 187, 1998.
    • [55] L. Hedin, S. Lundqvist, H. Ehrenrich, F. Seitz, and D. Turnbull. Solid State Physics, 28:225-300, 1973.
    • [56] M. Bennett and J. C. Inkson. J. Phys. C, 10(987), 1977.
    • [57] P. Hohenberg and W. Kohn. Phys. Rev., 136(B864), 1964.
    • [58] L. H. Thomas. Proc. Cambridge Philos. Soc., 23:542, 1927.
    • [59] E. Fermi. Z. Phys., 48(73), 1928.
    • [60] P. A. M. Dirac. Proc. Cambridge Philos. Soc., 26:376, 1930.
    • [61] W. Kohn and L. J. Sham. Phys. Rev., 140(A1133), 1965.
    • [62] J. P. Perdew and A. Zunger. Phys. Rev. B, 23(5048), 1981.
    • [63] P. M. Cepherley and B. J. Alder. Phys. Rev. Lett, 45(566), 1980.
    • [64] L. H. Yang, A. P. Smith, R. Benedek, and D. D. Koelling. Phys. Rev. B, 47(24): 16101-16106, 1993.
    • [65] J. P. Perdew and Y. Wang. Phys. Rev. B, 33(8800), 1986.
    • [66] A. D. Becke. J. Chem. Phys., 98(1372), 1993.
    • [67] A. D. Becke. Phys. Rev. A, 38(3098), 1988.
    • [68] J. Wang, A. Hallmark, D. S. Marshall, W. J. Ooms, P. Ordejon, J Junquera, D. Sanchez-Portal, E. Artacho, and J. M. Soler. Phys. Rev. B (Rapid Comm.), 60(4968), 1999.
    • [69] D. Sanchez-Portal, E. Artacho, J. M. Soler, A. Rubio, and P. Ordejon. Phys. Rev. B, 59(12678), 1999.
    • [70] M. S. C. Mazzoni and H. Chacham. Appl. Phys. Lett., 76:1561-1563, 2000.
    • [71] E. Burgos, E. Halac, R. Weht, H. Bonadeo, E. Artacho, and P. Ordejon. Phys. Rev. Lett., 85(2328), 2000.
    • [72] J. K. Tomfohr and O. F. Sankey. Phys. Stat. Sol. B, 233:59-69, 2002.
    • [73] X. D. Cui, A. Primak, X. Zarate, J. Tomfohr, O. F. Sankey, A. L. Moore, T. A. Moore, D. Gust, L. A. Nagahara, and S. M. Lindsay. J. Phys. Chem. B, 106:8609-8614, 2002.
    • [74] M. D. Towler and M. Causa. Computer Phys. Comms., 98:181-205, 1996.
    • [75] F. Q. Ban, K. N. Rankin, J. W. Gauld, and R. J. Boyd. Theor. Chem. Acc., 108(1):1-11, 2002.
    • [76] J. G. Kushmerick, D. B. Holt, J. C. Yang, J. Naciri, M. H. Moore, and R. Shashidhar. Phys. Rev. Lett., 89(8):086802, 2002.
    • [77] M. Kondo T. Tada and K. Yoshiyawa. Chem. Phys. Chem, 4(11), 2003.
    • [78] E. G. Emberly and G. Kirczenow. Phys. Rev. B, 58(16): 10911-10920, 1998.
    • [79] J.C. Slater and G.F. Koster. Phys. Rev., 94(6): 1498-1524, 1954.
    • [80] F. Bloch. Z. Physik, 52:555, 1928.
    • [81] R. Hoffmann. J. Chem. Phys., 39(6): 1397-1412, 1963.
    • [82] W. A. Harrison. Electronic structure and the properties of solids. Freeman, San Francisco, 1980.
    • [83] M. Nishida. Phys. Rev. B, 58(11):7103-7112, 1998.
    • [84] A. Ouammou, M. Mouallembahout, O. Pena, J. F. Halet, J. Y. Saillard, and C. Carel. J. Solid State Chem., 117(l):73-79, 1995.
    • [85] X. A. Chen, M. Onoda, H. Wada, A. Sato, H. Nozaki, and R. Herbst-Irmer. J. Solid State Chem., 145(1):204-211, 1999.
    • [86] M. S. Bailey and F. J. DiSalvo. J. Alloy. Compd., 353(1-2):146-152, 2003.
    • [87] J. F. Britten, O. P. Clements, R. C. Haddon, M. E. Itkis, K. M. Matkovich, and R. T. Oakley. Chem Mater, 16(8): 1564-1572, 2004.
    • [88] M. P. Samanta, W. Tian, and S. Datta. Phys. Rev. B, 53(12):7626-7629, 1996.
    • [90] M. Magoga and C Joachim. Phys. Rev. B, 56:4722-4729, 1997.
    • [91] M. Olson, Y. Mao, T. Windus, M. Kemp, M. Ratner, N Leon, and V. Mujica. J. Phys. Chem. B, 102:941-947, 1998.
    • [92] S. N. Yaliraki, M. Kemp, and M. A. Ratner. J. Am. Chem. Soc., 121:3428- 3434, 1999.
    • [93] J. Cerda and F. Soria. Phys. Rev. B, 61 (12):7965-7971, 2000.
    • [94] R. H. Dicke and J. P. Wittke. Introduction to quantum mechanics. AddisonWesley, page 148, 1963.
    • [95] D.M. Medvedev. J. Am. Chem., 122(28):6571-6582, 2000.
    • [96] R.R. Sharma. Phys. Rev. A, 13(2):3682-3693, 1976.
    • [97] H. Ibach and H. Liith. Solid-state physics. Springer-Verlag, Berlin: 168-171, 1993.
    • [99] J. E. Inglesfield, S. Crampin, and H. Ishida. Phys. Rev. B, (in press), 2005. [104] Yu. V. Sharvin. Soviet Phys. JETP, 21(655), 1965.
    • [117] S. Roche. Phys. Rev. Lett., 91(10), 2003.
    • [118] W. Zhang and S. E. Ulloa. Microelectronics Journal, 35:23-26, 2004.
    • [119] J. E. Inglesfield. Journal of Physics C-Solid State Physics, 14(26) :3795-3806, 1981.
    • [120] P. Ordejon, D. A. Drabold, M. P. Grumbach, and R. M. Martin. Phys. Rev. B, 48(19):14646-14649, 1993.
    • [121] X. P. Li, R. W. Nunes, and D. Vanderbilt. Phys. Rev. B, 47(16):10891-10894, 1993.
    • [122] S. Crampin, J. B. A. N. Van Hoof, and M. Nekovee. J. Phys.: Condens Matter, 4(1475), 1992.
    • [123] M. P. Anantram and T. R. Govindan. Phys. Rev. B, 58(8), 1998.
    • [124] J. H. Xu and A. J. Freeman. Phys. Rev. B, 40:11927, 1989.
    • [125] D. Wortmann, H. Ishida, and S. Bliigel. Phys. Rev. B, 66(075113), 2002.
    • [126] D. S. Fisher and P. A. Lee. Phys. Rev. B, 23(12):6851-6854, 1983.
    • [127] M. Brandbyge, N. Kobayashi, and M. Tsukada. Phys. Rev. B, 60(24):17064- 17070, 1999.
    • [128] A. Troisi and M. A. Ratner. J. Chem. Phys., 118(13):6072-6082, 2003.
    • [129] N. Agrai't, A. L. Yeyati, and J. M. van Ruitenbeek. Physics Reports, 377(81), 2003.
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